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Chapter 5
Character–Based Methods of
Phylogenetics
暨南大學資訊工程學系
黃光璿 (HUANG, Guan-Shieng)
2004/04/05
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5.1 Parsimony

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Mutations are exceedingly rare events.
The most unlikely events a model
invokes, the less likely the model is to
be correct.
 The fewest number of mutations to
explain a state is the most likely to be
correct.
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Ockham's Razor

the philosophic rule states that entities
should not be multiplied unnecessarily
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5.1.1 Informative and Uninformative Sites
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5.1.1 Informative and Uninformative Sites
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informative sites
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have information to construct a tree
uninformative sites

have no information
in the sense of parsimony principle.
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uninformative
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uninformative
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informative
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informative
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
A position to be informative must have
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at least two different nucleotides
each of these nucleotides to present at
least twice.
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
informative sites
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synapomorphy: support the internal
branches (true)
homoplasy: acquired as a result of parallel
evolution of convergence (false)

眼睛：humans, flies, mollusks (軟體動物)
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5.1.2 Unweighted Parsimony
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Every possible tree is considered
individually for each informative site.
The tree with the minimum overall
costs are reported.
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There are several problems:
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The number of alternative unrooted trees
increases dramatically.
Calculating the number of substitutions
invoked by each alternative tree is difficult.
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
The second problem can be solved by
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intersection: if the intersection of the two
sets of its children is not empty
union: if it is empty.
The number of unions is the minimum
number of substitutions.
 For uninformative site, it is the number
of different nucleotides minus one.

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/* the uth position in the kth sequence */
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5.1.4 Weighted Parsimony

Not all mutations are equivalent
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Some sequences (e.g., non-coding seq.)
are more prone to indel than others.
Functional importance differs from gene to
gene.
Subtle substitution biases usually vary
between genes and between species.
 Weights (scoring matrices) can be
added to reflect these differences.
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Calculating the optimal costs
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Finding the internal nodes
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5.2 Inferred Ancestral Sequences

Can be derived while constructing the
tree.

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 No missing link!
如何取樣本? It may be bias.
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5.3 Strategies for Faster Searches

The number of different phylogenetic
tree grows enormously.

10 sequences  2M for exhaustive search
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參考資料及圖片出處
1.
2.
3.
Fundamental Concepts of Bioinformatics
Dan E. Krane and Michael L. Raymer,
Benjamin/Cummings, 2003.
Biological Sequence Analysis
– Probabilistic models of proteins and
nucleic acids
R. Durbin, S. Eddy, A. Krogh, G.
Mitchison, Cambridge University Press,
1998.
Biology, by Sylvia S. Mader, 8th edition,
McGraw-Hill, 2003.
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